Variant report

Variant	rs56307925
Chromosome Location	chr19:40945618-40945619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40945235-40946818	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:40945070-40946567	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:40945186-40945733	U87	brain:	n/a	n/a
4	POLR2A	chr19:40945036-40947489	K562	blood:	n/a	n/a
5	POLR2A	chr19:40944883-40955137	K562	blood:	n/a	n/a
6	POLR2A	chr19:40945324-40945664	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:40945211-40946410	ProgFib	skin:	n/a	n/a
8	POLR2A	chr19:40945126-40947129	K562	blood:	n/a	n/a
9	POLR2A	chr19:40944976-40947714	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr19:40945468-40945751	A549	lung:	n/a	n/a
11	POLR2A	chr19:40945152-40945684	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr19:40945547-40945777	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:40945123-40946692	HCT-116	colon:	n/a	n/a
14	POLR2A	chr19:40945339-40945886	HepG2	liver:	n/a	n/a
15	JUND	chr19:40945172-40945798	A549	lung:	n/a	n/a
16	POLR2A	chr19:40945108-40946370	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr19:40945285-40946990	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr19:40945184-40945757	U87	brain:	n/a	n/a
19	POLR2A	chr19:40945105-40946367	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr19:40945351-40945687	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUND	chr19:40945067-40946719	A549	lung:	n/a	chr19:40946107-40946115
22	PBX3	chr19:40945188-40946301	A549	lung:	n/a	n/a
23	POLR2A	chr19:40945322-40947283	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:40945209-40950245	A549	lung:	n/a	n/a
25	POLR2A	chr19:40945179-40946747	GM12878	blood:	n/a	n/a
26	RUNX3	chr19:40945199-40945627	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:40945176-40945722	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:40945542-40945708	A549	lung:	n/a	n/a
29	POLR2A	chr19:40945206-40946956	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr19:40945137-40945897	U87	brain:	n/a	n/a
31	POLR2A	chr19:40945070-40945777	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr19:40945262-40946666	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr19:40945260-40945777	GM12892	blood:	n/a	n/a
34	MTA3	chr19:40945093-40946657	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:40945376-40945778	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:40945251-40945786	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr19:40945108-40946807	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr19:40945281-40945802	GM12892	blood:	n/a	n/a
39	POLR2A	chr19:40945467-40945712	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:40944978-40947626	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr19:40945218-40945786	K562	blood:	n/a	n/a
42	POLR2A	chr19:40945106-40945695	GM12891	blood:	n/a	n/a
43	POLR2A	chr19:40945117-40947505	GM12878	blood:	n/a	n/a
44	TCF12	chr19:40945180-40946852	A549	lung:	n/a	n/a
45	POLR2A	chr19:40945146-40945676	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr19:40945237-40945781	GM12891	blood:	n/a	n/a
47	BCL3	chr19:40945096-40946636	A549	lung:	n/a	n/a
48	POLR2A	chr19:40945463-40945714	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr19:40945131-40946508	U87	brain:	n/a	n/a
50	POLR2A	chr19:40945219-40946290	HCT-116	colon:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40930168..40933020-chr19:40943160..40946840,3	MCF-7	breast:
2	chr19:40937972..40941758-chr19:40943827..40946363,4	K562	blood:
3	chr19:40851266..40855955-chr19:40945466..40950850,6	K562	blood:
4	chr19:40945209..40947044-chr19:41022798..41025322,2	MCF-7	breast:
5	chr19:40930428..40932998-chr19:40942999..40947020,6	K562	blood:
6	chr19:40945484..40955522-chr19:40966442..40973559,31	MCF-7	breast:
7	chr19:40908387..40911091-chr19:40944867..40946978,2	MCF-7	breast:
8	chr19:40925098..40933993-chr19:40944045..40956524,41	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268366	TF binding region
ENSG00000090013	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000197019	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000160392	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11878466	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529139	1.00[EUR][1000 genomes]
rs7256097	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73559683	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
6	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
7	nsv911709	chr19:40928944-41060616	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40939600-40946000	Weak transcription	Gastric	stomach
2	chr19:40939800-40946000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:40939800-40946600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:40939800-40948200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:40939800-40948200	Weak transcription	Small Intestine	intestine
6	chr19:40940200-40946000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:40940200-40946000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:40940200-40946000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:40940200-40946000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:40940200-40946000	Weak transcription	HSMM	muscle
11	chr19:40940200-40946000	Weak transcription	NHEK	skin
12	chr19:40940200-40946200	Weak transcription	Fetal Kidney	kidney
13	chr19:40940200-40946400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:40940200-40946400	Weak transcription	Ovary	ovary
15	chr19:40940200-40946600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:40940200-40948000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr19:40940400-40945800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:40940400-40945800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:40940400-40946000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:40940400-40946000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:40940400-40946000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:40940400-40946000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:40940400-40946000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:40940400-40946000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:40940400-40946000	Weak transcription	Left Ventricle	heart
26	chr19:40940400-40946000	Weak transcription	Lung	lung
27	chr19:40940400-40946000	Weak transcription	NHDF-Ad	bronchial
28	chr19:40940400-40946000	Weak transcription	Osteobl	bone
29	chr19:40940400-40946200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:40940400-40946200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:40940400-40946200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr19:40940400-40946200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:40940400-40946200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:40940400-40946200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:40940400-40946200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:40940400-40946200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr19:40940400-40946200	Weak transcription	Fetal Brain Female	brain
38	chr19:40940400-40946200	Weak transcription	HSMMtube	muscle
39	chr19:40940400-40946200	Weak transcription	HUVEC	blood vessel
40	chr19:40940400-40946400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:40940400-40946400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:40940400-40946400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr19:40940400-40946400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:40940400-40946400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:40940400-40946400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:40940400-40946400	Weak transcription	Colonic Mucosa	Colon
47	chr19:40940400-40946400	Weak transcription	Esophagus	oesophagus
48	chr19:40940400-40946400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr19:40940400-40946400	Weak transcription	Right Ventricle	heart
50	chr19:40940400-40946400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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